The trace element composition of zircon, especially in tandem with U-Pb geochronology, has become a powerful tool for tracing magmatic processes associated with the formation of porphyry copper deposits. However, the use of the redox-sensitive Eu and Ce anomalies as a potential mineral exploration proxy is controversial. This study presents a comprehensive, temporally constrained data set of zircon trace element compositions (n = 645) for three compositionally distinct magmatic series identified in the Meghri-Ordubad pluton, southernmost Lesser Caucasus. The 30 million years of Cenozoic magmatism in the Meghri-Ordubad pluton are associated with several ore-forming pulses leading to the formation of porphyry copper deposits and epithermal-style mineralization. Our zircon geochemical data constrain the thermal and chemical evolution of this complex intrusive suite and allow an evaluation of the usefulness of zircon as a mineral exploration proxy for porphyry copper deposits. Our results combined with Rayleigh fractionation modeling indicate that the trace element composition of zircon (Th/U, Hf, Ti, YbN/DyN, Eu anomalies) is influenced by the composition and the water concentration of the parental magma, as well as by co-crystallizing titanite and apatite. In contrast, the variations of Ce anomalies remain difficult to explain by magmatic processes and could rather be ascribed to relative fluctuations of the redox conditions. In the Meghri-Ordubad pluton, we do not observe any systematic patterns between the trace element composition in zircons and the different ore-forming pulses. This questions the reliability of using the trace element composition in zircon as an exploration mineral proxy, and it rather emphasizes that a good knowledge of the entire magmatic evolution of a metallogenic province is required.